Run environment for the Antibody Variant Designer block: AntiFold inverse folding (torch + torch_geometric), Sapiens humanness (transformers), SASA exposure (freesasa) and promb.

Everything is pinned explicitly. A variant does not inherit the base environment's dependency list, so the whole runtime closure is named here — it was resolved with uv pip compile --universal from the block's two exported requirement sets and then written out flat.

Every package with a loose requirement of its own is under noDeps. The builder resolves each declared package's closure separately, so any package that asks for a bare numpy or scipy pulls the newest one on top of the pins and vendors a second copy — numpy 2.5.3 beside 1.26.4, scipy 1.18.1 beside 1.16.3, and earlier also pandas 3, torch 2.14 and transformers 5. The import checker installs from that directory and takes the newest wheel a requirement allows, so it built its test venv on numpy 2 and every numpy-1-ABI extension in the set failed, biotite loudest at 24 modules.

Naming the whole closure flat is what makes noDeps safe here: nothing needs resolving, because everything any of these packages imports is already pinned above.

The biotite entries in checker/whitelists/*.json cover that same numpy-2 ABI error. With the noDeps set above they should never fire — they are there so one loose requirement slipping back in cannot fail five platforms again.

torch is declared per platform rather than in the shared list. On linux-x64 the PyPI wheel depends on twelve nvidia-* CUDA packages worth roughly 2 GiB that this block never uses, so that platform takes torch==2.2.2+cpu from https://download.pytorch.org/whl/cpu, which the shared config already lists as an additional registry. The macOS and Windows PyPI wheels are CPU builds already, and the nvidia-* requirements are marked linux-x86_64 only, so those platforms take the plain pin.

freesasa publishes no cp312 wheel on any platform and never has, so it is built on the runner for all five, exactly as the base 3.12.10 environment does it.

biotite is at 0.39.0 rather than the 0.38.* the block's pyproject.toml asks for: 0.38 predates cp312 and publishes no wheel any Python 3.12 can use, so pinning it would mean a source build on all five platforms, Windows included. 0.39.0 is the first line with cp312 wheels. The block's bound has to move with this.

biotite has no Linux ARM64 wheel for any version, so that one platform compiles its Cython sources on the native ARM runner.